You should be fine. Go ahead and flash.
But first, what router do you have?
But, if you are really partial to your current configuration/scripts, make a backup.
I do not recommend restoring from backup myself. If there are issues after updating that cannot be fully resolved (ask away on the forums here as appropriate, in the proper thread), then I would simply 'Format the JFFS partition on next boot', format the USB drive on a PC and start again to have the most stable 'script' platform going forward.
But first steps first. Flash to the latest firmware and monitor your router, network, and scripts for proper operation.
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